forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1061 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
bb5cfe2b70
commit
721cd16798
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@ -31,8 +31,6 @@
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<LI>delta = thickness of spatial layers in dim (distance units)
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<LI>file = filename to write results to (NULL = no file)
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<LI>style = <I>density</I> or <I>compute</I> or <I>fix</I>
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<PRE> <I>density</I> arg = <I>mass</I> or <I>number</I>
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@ -43,25 +41,32 @@
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</PRE>
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<LI>zero or more keyword/value pairs may be appended
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<PRE>keyword = <I>norm</I> or <I>units</I>
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<LI>keyword = <I>norm</I> or <I>units</I> or <I>file</I> or <I>ave</I>
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<PRE> <I>units</I> value = <I>box</I> or <I>lattice</I> or <I>reduced</I>
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<I>norm</I> value = <I>all</I> or <I>sample</I>
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<I>units</I> value = <I>box</I> or <I>lattice</I> or <I>reduced</I>
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<I>file</I> arg = filename
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filename = file to write results to
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<I>ave</I> args = <I>one</I> or <I>running</I> or <I>window M</I>
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one = output new average value every Nfreq steps
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running = output cummulative average of all previous Nfreq steps
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window M = output average of M most recent Nfreq steps
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</PRE>
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>fix 1 all ave/spatial 10000 1 10000 z lower 2.0 centro.profile compute myCentro
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fix 1 flow ave/spatial 100 10 1000 y 0.0 1.0 vel.profile compute Vx norm sample
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fix 1 flow ave/spatial 100 5 1000 y 0.0 2.5 dens.profile density mass
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<PRE>fix 1 all ave/spatial 10000 1 10000 z lower 0.02 compute myCentro units reduced
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fix 1 flow ave/spatial 100 10 1000 y 0.0 1.0 compute Vx norm sample file vel.profile
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fix 1 flow ave/spatial 100 5 1000 y 0.0 2.5 density mass ave running
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Calculate one or more instantaneous per-atom quantities every few
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timesteps, average them by layer in a chosen dimension and over a
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longer timescale. The resulting averages can be written to a file
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and/or used by other <A HREF = "Section_howto.html#4_15">output commands</A> such as
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<A HREF = "thermo_style.html">thermo_style custom</A>.
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longer timescale. The resulting averages can be used by other <A HREF = "Section_howto.html#4_15">output
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commands</A> such as <A HREF = "thermo_style.html">thermo_style
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custom</A>, and also written to a file.
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</P>
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<P>This fix can be used to spatially average per-atom properties
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(velocity, force) or per-atom quantities calculated by a
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@ -70,14 +75,14 @@ and/or used by other <A HREF = "Section_howto.html#4_15">output commands</A> suc
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equation you define (see the <A HREF = "compute_variable_atom.html">compute
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variable/atom</A> command).
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</P>
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<P>The <I>density</I> styles means to simply count the number of atoms in each
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layer, either by mass or number. The <I>compute</I> style allows
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specification of a <A HREF = "compute.html">compute</A> which will be invoked to
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calculate the desired property. The compute can be previously defined
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in the input script or it can be a compute defined by a <A HREF = "dump.html">dump
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custom</A> command.
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<P>For style <I>density</I>, the number of atoms in each layer is counted,
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either by mass or by number. The <I>compute</I> style allows specification
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of a <A HREF = "compute.html">compute</A> which will be invoked to calculate the
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desired property. The compute can be previously defined in the input
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script or it can be a compute defined by a <A HREF = "dump.html">dump custom</A>
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command.
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</P>
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<P>For the <I>compute</I> style, the fix ave/spatial command accesses the
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<P>For style <I>compute</I>, the fix ave/spatial command accesses the
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per-atom scalar or vector values stored by the compute. Thus it must
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be a "per-atom" compute with the word "atom" in its style name, rather
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than a "global" compute. See the <A HREF = "fix_ave_time.html">fix ave/time</A>
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@ -95,28 +100,41 @@ per-atom compute styles and <A HREF = "Section_modify.html">add them to LAMMPS</
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Note that the <A HREF = "dump.html">dump custom</A> command can also be used to
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directly output per-atom quantities calculated by a per-atom compute.
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</P>
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<P>For the <I>fix</I> style, the fix ave/spatial command accesses the per-atom
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<P>For style <I>fix</I>, the fix ave/spatial command accesses the per-atom
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scalar or vector values stored by another fix. The <A HREF = "fix_ave_atom.html">fix
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ave/atom</A> command is an example of such a fix.
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</P>
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<P>In all cases, the calculated property is averaged over atoms in each
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layer, where the layers are in a particular <I>dim</I> and have a thickness
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given by <I>delta</I>. Every Nfreq steps, when a property is calculated
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for the first time (after a previous write), the number of layers and
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the layer boundaries are computed. Thus if the simlation box changes
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size during a simulation, the number of layers and their boundaries
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may also change. Layers are defined relative to a specified <I>origin</I>,
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which may be the lower/upper edge of the box (in <I>dim</I>) or its center
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point, or a specified coordinate value. Starting at the origin,
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sufficient layers are created in both directions to completely cover
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the box. On subsequent timesteps every atom is mapped to one of the
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layers. Atoms beyond the lowermost/uppermost layer are counted in the
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first/last layer.
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<P>The <I>Nevery</I>, <I>Nrepeat</I>, and <I>Nfreq</I> arguments specify on what
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timesteps the per-atom property will be evaluated in order to
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contribute to the average. The final averaged values are computed
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every <I>Nfreq</I> timesteps. The average is over <I>Nrepeat</I> values,
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computed in the preceeding portion of the simulation every <I>Nevery</I>
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timesteps. <I>Nfreq</I> must be a multiple of <I>Nevery</I> and <I>Nevery</I> must
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be non-zero even if <I>Nrepeat</I> is 1.
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</P>
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<P>For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
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timesteps 90,92,94,96,98,100 will be used to compute the final average
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on timestep 100. Similary for timesteps 190,192,194,196,198,200 on
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timestep 200, etc.
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</P>
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<P>The per-atom property is also averaged over atoms in each layer, where
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the layers are in a particular <I>dim</I> and have a thickness given by
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<I>delta</I>. Every Nfreq steps, when an averaging is being performed and
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the per-atom property is calculated for the first time, the number of
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layers and the layer boundaries are computed. Thus if the simlation
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box changes size during a simulation, the number of layers and their
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boundaries may also change. Layers are defined relative to a
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specified <I>origin</I>, which may be the lower/upper edge of the box (in
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<I>dim</I>) or its center point, or a specified coordinate value. Starting
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at the origin, sufficient layers are created in both directions to
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completely cover the box. On subsequent timesteps every atom is
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mapped to one of the layers. Atoms beyond the lowermost/uppermost
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layer are counted in the first/last layer.
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</P>
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<P>For orthogonal simulation boxes, the layers are "slices" aligned with
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the xyz coordinate axes. For non-orthogonal (triclinic) simulation
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boxes, the layers are "tilted slices" that align with the tilted faces
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of the box. See the <A HREF = "region.html">region prism</A> command for a
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boxes, the layers are "tilted slices" that are parallel to the tilted
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faces of the box. See the <A HREF = "region.html">region prism</A> command for a
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discussion of the geometry of tilted boxes in LAMMPS. As described
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there, a tilted simulation box has edge vectors a,b,c. In that
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nomenclature, layers in the x dimension have faces with normals in the
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@ -124,12 +142,26 @@ nomenclature, layers in the x dimension have faces with normals in the
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cross "c" direction. And layers in z have faces normal to the "a"
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cross "b" direction. Note that in order to define the thickness and
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position of these tilted layers in an unambiguous fashion, the <I>units</I>
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option must be set to <I>reduced</I>.
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option must be set to <I>reduced</I> when using a non-orthogonal simulation
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box, as discussed below.
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</P>
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<P>For the <I>compute</I> and <I>fix</I> keywords, the per-atom calculation
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performed by the compute or fix is on the group defined by that
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command. However, only atoms in the fix group are included in the
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layer averaging.
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</P>
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<P>Note that some computes perform costly calculations, involving the
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creation or use of neighbor lists. If the compute is invoked too
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often by fix ave/spatial, it can slow down a simulation.
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</P>
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<HR>
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<P>Additional optional keywords also affect the operation of this fix.
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</P>
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<P>The <I>units</I> keyword determines the meaning of the distance units used
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for the layer thickness <I>delta</I> and for <I>origin</I> if it is a coordinate
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value. For orthogonal simulation boxes, any of the 3 options may be
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used. For non-orthongal (triclinic) simulation boxes, only the
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used. For non-orthogonal (triclinic) simulation boxes, only the
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<I>reduced</I> option may be used.
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</P>
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<P>A <I>box</I> value selects standard distance units as defined by the
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@ -149,52 +181,64 @@ the lower "b" cross "c" plane of the simulation box and an <I>origin</I> of
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A <I>delta</I> value of 0.1 means there will be 10 layers from 0.0 to 1.0,
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regardless of the current size or shape of the simulation box.
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</P>
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<P>The <I>Nevery</I>, <I>Nrepeat</I>, and <I>Nfreq</I> arguments specify how the
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property will be time-averaged. The final averaged value(s) are
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computed every <I>Nfreq</I> timesteps. The average is over <I>Nrepeat</I>
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values, computed in the preceeding portion of the simulation every
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<I>Nevery</I> timesteps. Thus if Nevery=2, Nrepeat=6, and Nfreq=100, then
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values on timesteps 90,92,94,96,98,100 will be used to compute the
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final average on timestep 100. Similary for timesteps
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190,192,194,196,198,200 on timestep 200, etc.
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</P>
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<P>The <I>norm</I> keyword also affects how time-averaging is done. For an
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<I>all</I> setting, a layer quantity is summed over all atoms in all
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Nfreq/Nevery samples, as is the count of atoms in the layer. The
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printed value for the layer is Total-quantity / Total-count.
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In other words it is an average over the entire Nfreq timescale.
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<P>The <I>norm</I> keyword affects how time-averaging is done within for the
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output produced every <I>Nfreq</I> timesteps. For an <I>all</I> setting, a
|
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layer quantity is summed over all atoms in all <I>Nrepeat</I> samples, as
|
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is the count of atoms in the layer. The printed value for the layer
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is Total-quantity / Total-count. In other words it is an average over
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the entire <I>Nfreq</I> timescale.
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</P>
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<P>For a <I>sample</I> setting, the quantity is summed over atoms for only a
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single sample, as is the count, and a "average sample value" is
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computed, i.e. Sample-quantity / Sample-count. The printed value for
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the layer is the average of the M "average sample values", where M =
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Nfreq/Nevery. In other words it is an average of an average.
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the layer is the average of the <I>Nrepeat</I> "average sample values", In
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other words it is an average of an average.
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</P>
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<P>If file output is specified, each time info is written to the file, it
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is in the following format. A line with the timestep and number of
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layers is written. Then one line per layer is written, containing the
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layer ID (1-N), the coordinate of the center of the layer, the number
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of atoms in the layer, and one or more calculated values. The number
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of atoms and the value(s) are average quantities. If the value of the
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<I>units</I> keyword is <I>box</I> or <I>lattice</I>, the "coord" is printed in box
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units. If the value of the <I>units</I> keyword is <I>reduced</I>, the "coord"
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is printed in reduced units (0-1).
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<P>The <I>file</I> keyword allows a filename to be specified. Every <I>Nfreq</I>
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timesteps, layer info will be written to a text file in the following
|
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format. A line with the timestep and number of layers is written.
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Then one line per layer is written, containing the layer ID (1-N), the
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coordinate of the center of the layer, the number of atoms in the
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layer, and one or more calculated values. The number of atoms and the
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value(s) are average quantities. If the value of the <I>units</I> keyword
|
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is <I>box</I> or <I>lattice</I>, the "coord" is printed in box units. If the
|
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value of the <I>units</I> keyword is <I>reduced</I>, the "coord" is printed in
|
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reduced units (0-1).
|
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</P>
|
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<P>If the <I>density</I> keyword is used, or the <I>compute</I> or <I>fix</I> keyword
|
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with a compute/fix that calculates a single quantity per atom, then a
|
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single value will be printed for each layer. If the <I>compute</I> or
|
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<I>fix</I> keyword is used with a compute/fix that calculates N quantities
|
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per atom, then N values per line will be written, each of them
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averaged independently.
|
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<P>If the style is <I>density</I>, or the style is <I>compute</I> or <I>fix</I> with a
|
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compute/fix that calculates a single quantity per atom, then a single
|
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value will be printed for each layer. If the style is <I>compute</I> or
|
||||
<I>fix</I> with a compute/fix that calculates N quantities per atom, then N
|
||||
values per line will be written, each of them averaged independently.
|
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</P>
|
||||
<P>For the <I>compute</I> and <I>fix</I> keywords, the calculation performed by the
|
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compute or fix is on the group defined by the that command. However,
|
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only atoms in the fix group are included in the layer averaging.
|
||||
<P>The <I>ave</I> keyword determines how the layer values produced every
|
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<I>Nfreq</I> steps are averaged with layer values produced on previous
|
||||
steps that were multiples of <I>Nfreq</I>, before they are accessed by
|
||||
another output command or written to a file.
|
||||
</P>
|
||||
<P>Note that some computes perform costly calculations, involving use of
|
||||
or creation of neighbor lists. If the compute is invoked too often by
|
||||
fix ave/spatial, it can slow down a simulation.
|
||||
<P>If the <I>ave</I> setting is <I>one</I>, then the layuer values produced on
|
||||
timesteps that are multiples of <I>Nfreq</I> are independent of each other;
|
||||
they are output as-is without further averaging.
|
||||
</P>
|
||||
<P>If the <I>ave</I> setting is <I>running</I>, then the layer values produced on
|
||||
timesteps that are multiples of <I>Nfreq</I> are summed and averaged in a
|
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cummulative sense before being output. Each output layer value is
|
||||
thus the average of the layer value produced on that timestep with all
|
||||
preceeding values for the same layer. This running average begins
|
||||
when the fix is defined; it can only be restarted by deleting the fix
|
||||
via the <A HREF = "unfix.html">unfix</A> command, or re-defining the fix by
|
||||
re-specifying it.
|
||||
</P>
|
||||
<P>If the <I>ave</I> setting is <I>window</I>, then the layer values produced on
|
||||
timesteps that are multiples of <I>Nfreq</I> are summed and averaged within
|
||||
a moving "window" of time, so that the last M values for the same
|
||||
layer are used to produce the output. E.g. if M = 3 and Nfreq = 1000,
|
||||
then the output on step 10000 will be the average of the individual
|
||||
layer values on steps 8000,9000,10000. Outputs on early steps will
|
||||
average over less than M values if they are not available.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
|
||||
</P>
|
||||
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
|
||||
|
|
@ -224,6 +268,7 @@ minimization</A>.
|
|||
</P>
|
||||
<P><B>Default:</B>
|
||||
</P>
|
||||
<P>The option defaults are norm = all and units = lattice.
|
||||
<P>The option defaults are units = lattice, norm = all, no file output,
|
||||
and ave = one.
|
||||
</P>
|
||||
</HTML>
|
||||
|
|
|
|||
|
|
@ -20,7 +20,6 @@ Nfreq = timestep frequency at which the average value is computed :l
|
|||
dim = {x} or {y} or {z} :l
|
||||
origin = {lower} or {center} or {upper} or coordinate value (distance units) :l
|
||||
delta = thickness of spatial layers in dim (distance units) :l
|
||||
file = filename to write results to (NULL = no file) :l
|
||||
style = {density} or {compute} or {fix} :l
|
||||
{density} arg = {mass} or {number}
|
||||
{mass} = compute mass density
|
||||
|
|
@ -28,24 +27,30 @@ style = {density} or {compute} or {fix} :l
|
|||
{compute} arg = compute-ID that stores or calculates per-atom quantities
|
||||
{fix} arg = fix-ID that stores or calculates per-atom quantities :pre
|
||||
zero or more keyword/value pairs may be appended :l
|
||||
keyword = {norm} or {units}
|
||||
keyword = {norm} or {units} or {file} or {ave} :l
|
||||
{units} value = {box} or {lattice} or {reduced}
|
||||
{norm} value = {all} or {sample}
|
||||
{units} value = {box} or {lattice} or {reduced} :pre
|
||||
{file} arg = filename
|
||||
filename = file to write results to
|
||||
{ave} args = {one} or {running} or {window M}
|
||||
one = output new average value every Nfreq steps
|
||||
running = output cummulative average of all previous Nfreq steps
|
||||
window M = output average of M most recent Nfreq steps :pre
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
fix 1 all ave/spatial 10000 1 10000 z lower 2.0 centro.profile compute myCentro
|
||||
fix 1 flow ave/spatial 100 10 1000 y 0.0 1.0 vel.profile compute Vx norm sample
|
||||
fix 1 flow ave/spatial 100 5 1000 y 0.0 2.5 dens.profile density mass :pre
|
||||
fix 1 all ave/spatial 10000 1 10000 z lower 0.02 compute myCentro units reduced
|
||||
fix 1 flow ave/spatial 100 10 1000 y 0.0 1.0 compute Vx norm sample file vel.profile
|
||||
fix 1 flow ave/spatial 100 5 1000 y 0.0 2.5 density mass ave running :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Calculate one or more instantaneous per-atom quantities every few
|
||||
timesteps, average them by layer in a chosen dimension and over a
|
||||
longer timescale. The resulting averages can be written to a file
|
||||
and/or used by other "output commands"_Section_howto.html#4_15 such as
|
||||
"thermo_style custom"_thermo_style.html.
|
||||
longer timescale. The resulting averages can be used by other "output
|
||||
commands"_Section_howto.html#4_15 such as "thermo_style
|
||||
custom"_thermo_style.html, and also written to a file.
|
||||
|
||||
This fix can be used to spatially average per-atom properties
|
||||
(velocity, force) or per-atom quantities calculated by a
|
||||
|
|
@ -54,14 +59,14 @@ This fix can be used to spatially average per-atom properties
|
|||
equation you define (see the "compute
|
||||
variable/atom"_compute_variable_atom.html command).
|
||||
|
||||
The {density} styles means to simply count the number of atoms in each
|
||||
layer, either by mass or number. The {compute} style allows
|
||||
specification of a "compute"_compute.html which will be invoked to
|
||||
calculate the desired property. The compute can be previously defined
|
||||
in the input script or it can be a compute defined by a "dump
|
||||
custom"_dump.html command.
|
||||
For style {density}, the number of atoms in each layer is counted,
|
||||
either by mass or by number. The {compute} style allows specification
|
||||
of a "compute"_compute.html which will be invoked to calculate the
|
||||
desired property. The compute can be previously defined in the input
|
||||
script or it can be a compute defined by a "dump custom"_dump.html
|
||||
command.
|
||||
|
||||
For the {compute} style, the fix ave/spatial command accesses the
|
||||
For style {compute}, the fix ave/spatial command accesses the
|
||||
per-atom scalar or vector values stored by the compute. Thus it must
|
||||
be a "per-atom" compute with the word "atom" in its style name, rather
|
||||
than a "global" compute. See the "fix ave/time"_fix_ave_time.html
|
||||
|
|
@ -79,28 +84,41 @@ per-atom compute styles and "add them to LAMMPS"_Section_modify.html.
|
|||
Note that the "dump custom"_dump.html command can also be used to
|
||||
directly output per-atom quantities calculated by a per-atom compute.
|
||||
|
||||
For the {fix} style, the fix ave/spatial command accesses the per-atom
|
||||
For style {fix}, the fix ave/spatial command accesses the per-atom
|
||||
scalar or vector values stored by another fix. The "fix
|
||||
ave/atom"_fix_ave_atom.html command is an example of such a fix.
|
||||
|
||||
In all cases, the calculated property is averaged over atoms in each
|
||||
layer, where the layers are in a particular {dim} and have a thickness
|
||||
given by {delta}. Every Nfreq steps, when a property is calculated
|
||||
for the first time (after a previous write), the number of layers and
|
||||
the layer boundaries are computed. Thus if the simlation box changes
|
||||
size during a simulation, the number of layers and their boundaries
|
||||
may also change. Layers are defined relative to a specified {origin},
|
||||
which may be the lower/upper edge of the box (in {dim}) or its center
|
||||
point, or a specified coordinate value. Starting at the origin,
|
||||
sufficient layers are created in both directions to completely cover
|
||||
the box. On subsequent timesteps every atom is mapped to one of the
|
||||
layers. Atoms beyond the lowermost/uppermost layer are counted in the
|
||||
first/last layer.
|
||||
The {Nevery}, {Nrepeat}, and {Nfreq} arguments specify on what
|
||||
timesteps the per-atom property will be evaluated in order to
|
||||
contribute to the average. The final averaged values are computed
|
||||
every {Nfreq} timesteps. The average is over {Nrepeat} values,
|
||||
computed in the preceeding portion of the simulation every {Nevery}
|
||||
timesteps. {Nfreq} must be a multiple of {Nevery} and {Nevery} must
|
||||
be non-zero even if {Nrepeat} is 1.
|
||||
|
||||
For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
|
||||
timesteps 90,92,94,96,98,100 will be used to compute the final average
|
||||
on timestep 100. Similary for timesteps 190,192,194,196,198,200 on
|
||||
timestep 200, etc.
|
||||
|
||||
The per-atom property is also averaged over atoms in each layer, where
|
||||
the layers are in a particular {dim} and have a thickness given by
|
||||
{delta}. Every Nfreq steps, when an averaging is being performed and
|
||||
the per-atom property is calculated for the first time, the number of
|
||||
layers and the layer boundaries are computed. Thus if the simlation
|
||||
box changes size during a simulation, the number of layers and their
|
||||
boundaries may also change. Layers are defined relative to a
|
||||
specified {origin}, which may be the lower/upper edge of the box (in
|
||||
{dim}) or its center point, or a specified coordinate value. Starting
|
||||
at the origin, sufficient layers are created in both directions to
|
||||
completely cover the box. On subsequent timesteps every atom is
|
||||
mapped to one of the layers. Atoms beyond the lowermost/uppermost
|
||||
layer are counted in the first/last layer.
|
||||
|
||||
For orthogonal simulation boxes, the layers are "slices" aligned with
|
||||
the xyz coordinate axes. For non-orthogonal (triclinic) simulation
|
||||
boxes, the layers are "tilted slices" that align with the tilted faces
|
||||
of the box. See the "region prism"_region.html command for a
|
||||
boxes, the layers are "tilted slices" that are parallel to the tilted
|
||||
faces of the box. See the "region prism"_region.html command for a
|
||||
discussion of the geometry of tilted boxes in LAMMPS. As described
|
||||
there, a tilted simulation box has edge vectors a,b,c. In that
|
||||
nomenclature, layers in the x dimension have faces with normals in the
|
||||
|
|
@ -108,12 +126,26 @@ nomenclature, layers in the x dimension have faces with normals in the
|
|||
cross "c" direction. And layers in z have faces normal to the "a"
|
||||
cross "b" direction. Note that in order to define the thickness and
|
||||
position of these tilted layers in an unambiguous fashion, the {units}
|
||||
option must be set to {reduced}.
|
||||
option must be set to {reduced} when using a non-orthogonal simulation
|
||||
box, as discussed below.
|
||||
|
||||
For the {compute} and {fix} keywords, the per-atom calculation
|
||||
performed by the compute or fix is on the group defined by that
|
||||
command. However, only atoms in the fix group are included in the
|
||||
layer averaging.
|
||||
|
||||
Note that some computes perform costly calculations, involving the
|
||||
creation or use of neighbor lists. If the compute is invoked too
|
||||
often by fix ave/spatial, it can slow down a simulation.
|
||||
|
||||
:line
|
||||
|
||||
Additional optional keywords also affect the operation of this fix.
|
||||
|
||||
The {units} keyword determines the meaning of the distance units used
|
||||
for the layer thickness {delta} and for {origin} if it is a coordinate
|
||||
value. For orthogonal simulation boxes, any of the 3 options may be
|
||||
used. For non-orthongal (triclinic) simulation boxes, only the
|
||||
used. For non-orthogonal (triclinic) simulation boxes, only the
|
||||
{reduced} option may be used.
|
||||
|
||||
A {box} value selects standard distance units as defined by the
|
||||
|
|
@ -133,51 +165,63 @@ the lower "b" cross "c" plane of the simulation box and an {origin} of
|
|||
A {delta} value of 0.1 means there will be 10 layers from 0.0 to 1.0,
|
||||
regardless of the current size or shape of the simulation box.
|
||||
|
||||
The {Nevery}, {Nrepeat}, and {Nfreq} arguments specify how the
|
||||
property will be time-averaged. The final averaged value(s) are
|
||||
computed every {Nfreq} timesteps. The average is over {Nrepeat}
|
||||
values, computed in the preceeding portion of the simulation every
|
||||
{Nevery} timesteps. Thus if Nevery=2, Nrepeat=6, and Nfreq=100, then
|
||||
values on timesteps 90,92,94,96,98,100 will be used to compute the
|
||||
final average on timestep 100. Similary for timesteps
|
||||
190,192,194,196,198,200 on timestep 200, etc.
|
||||
|
||||
The {norm} keyword also affects how time-averaging is done. For an
|
||||
{all} setting, a layer quantity is summed over all atoms in all
|
||||
Nfreq/Nevery samples, as is the count of atoms in the layer. The
|
||||
printed value for the layer is Total-quantity / Total-count.
|
||||
In other words it is an average over the entire Nfreq timescale.
|
||||
The {norm} keyword affects how time-averaging is done within for the
|
||||
output produced every {Nfreq} timesteps. For an {all} setting, a
|
||||
layer quantity is summed over all atoms in all {Nrepeat} samples, as
|
||||
is the count of atoms in the layer. The printed value for the layer
|
||||
is Total-quantity / Total-count. In other words it is an average over
|
||||
the entire {Nfreq} timescale.
|
||||
|
||||
For a {sample} setting, the quantity is summed over atoms for only a
|
||||
single sample, as is the count, and a "average sample value" is
|
||||
computed, i.e. Sample-quantity / Sample-count. The printed value for
|
||||
the layer is the average of the M "average sample values", where M =
|
||||
Nfreq/Nevery. In other words it is an average of an average.
|
||||
the layer is the average of the {Nrepeat} "average sample values", In
|
||||
other words it is an average of an average.
|
||||
|
||||
If file output is specified, each time info is written to the file, it
|
||||
is in the following format. A line with the timestep and number of
|
||||
layers is written. Then one line per layer is written, containing the
|
||||
layer ID (1-N), the coordinate of the center of the layer, the number
|
||||
of atoms in the layer, and one or more calculated values. The number
|
||||
of atoms and the value(s) are average quantities. If the value of the
|
||||
{units} keyword is {box} or {lattice}, the "coord" is printed in box
|
||||
units. If the value of the {units} keyword is {reduced}, the "coord"
|
||||
is printed in reduced units (0-1).
|
||||
The {file} keyword allows a filename to be specified. Every {Nfreq}
|
||||
timesteps, layer info will be written to a text file in the following
|
||||
format. A line with the timestep and number of layers is written.
|
||||
Then one line per layer is written, containing the layer ID (1-N), the
|
||||
coordinate of the center of the layer, the number of atoms in the
|
||||
layer, and one or more calculated values. The number of atoms and the
|
||||
value(s) are average quantities. If the value of the {units} keyword
|
||||
is {box} or {lattice}, the "coord" is printed in box units. If the
|
||||
value of the {units} keyword is {reduced}, the "coord" is printed in
|
||||
reduced units (0-1).
|
||||
|
||||
If the {density} keyword is used, or the {compute} or {fix} keyword
|
||||
with a compute/fix that calculates a single quantity per atom, then a
|
||||
single value will be printed for each layer. If the {compute} or
|
||||
{fix} keyword is used with a compute/fix that calculates N quantities
|
||||
per atom, then N values per line will be written, each of them
|
||||
averaged independently.
|
||||
If the style is {density}, or the style is {compute} or {fix} with a
|
||||
compute/fix that calculates a single quantity per atom, then a single
|
||||
value will be printed for each layer. If the style is {compute} or
|
||||
{fix} with a compute/fix that calculates N quantities per atom, then N
|
||||
values per line will be written, each of them averaged independently.
|
||||
|
||||
For the {compute} and {fix} keywords, the calculation performed by the
|
||||
compute or fix is on the group defined by the that command. However,
|
||||
only atoms in the fix group are included in the layer averaging.
|
||||
The {ave} keyword determines how the layer values produced every
|
||||
{Nfreq} steps are averaged with layer values produced on previous
|
||||
steps that were multiples of {Nfreq}, before they are accessed by
|
||||
another output command or written to a file.
|
||||
|
||||
Note that some computes perform costly calculations, involving use of
|
||||
or creation of neighbor lists. If the compute is invoked too often by
|
||||
fix ave/spatial, it can slow down a simulation.
|
||||
If the {ave} setting is {one}, then the layuer values produced on
|
||||
timesteps that are multiples of {Nfreq} are independent of each other;
|
||||
they are output as-is without further averaging.
|
||||
|
||||
If the {ave} setting is {running}, then the layer values produced on
|
||||
timesteps that are multiples of {Nfreq} are summed and averaged in a
|
||||
cummulative sense before being output. Each output layer value is
|
||||
thus the average of the layer value produced on that timestep with all
|
||||
preceeding values for the same layer. This running average begins
|
||||
when the fix is defined; it can only be restarted by deleting the fix
|
||||
via the "unfix"_unfix.html command, or re-defining the fix by
|
||||
re-specifying it.
|
||||
|
||||
If the {ave} setting is {window}, then the layer values produced on
|
||||
timesteps that are multiples of {Nfreq} are summed and averaged within
|
||||
a moving "window" of time, so that the last M values for the same
|
||||
layer are used to produce the output. E.g. if M = 3 and Nfreq = 1000,
|
||||
then the output on step 10000 will be the average of the individual
|
||||
layer values on steps 8000,9000,10000. Outputs on early steps will
|
||||
average over less than M values if they are not available.
|
||||
|
||||
:line
|
||||
|
||||
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||
|
||||
|
|
@ -208,4 +252,5 @@ minimization"_minimize.html.
|
|||
|
||||
[Default:]
|
||||
|
||||
The option defaults are norm = all and units = lattice.
|
||||
The option defaults are units = lattice, norm = all, no file output,
|
||||
and ave = one.
|
||||
|
|
|
|||
|
|
@ -37,8 +37,6 @@
|
|||
scalar = single scalar value from fix or compute
|
||||
vector = vector of values from fix or compute
|
||||
both = both a single value and vector of values from fix or compute
|
||||
<I>file</I> arg = filename
|
||||
filename = file to write results to
|
||||
<I>ave</I> args = <I>one</I> or <I>running</I> or <I>window M</I>
|
||||
one = output new average value every Nfreq steps
|
||||
running = output cummulative average of all previous Nfreq steps
|
||||
|
|
@ -102,7 +100,7 @@ timestep 200, etc.
|
|||
</P>
|
||||
<HR>
|
||||
|
||||
<P>Additional optional keywords also affect the averaging.
|
||||
<P>Additional optional keywords also affect the operation of this fix.
|
||||
</P>
|
||||
<P>The <I>type</I> keyword chooses whether the scalar and/or vector quantities
|
||||
produced by the compute or fix are used. For a setting of <I>scalar</I> a
|
||||
|
|
@ -117,8 +115,9 @@ and/or N vector quantities are written to the file in a
|
|||
self-explanatory text format.
|
||||
</P>
|
||||
<P>The <I>ave</I> keyword determines how the scalar and/or vector values
|
||||
produced every <I>Nfreq</I> steps are averaged with each other before they
|
||||
are accessed by another output command or written to a file.
|
||||
produced every <I>Nfreq</I> steps are averaged with values produced on
|
||||
previous steps that were multiples of <I>Nfreq</I>, before they are
|
||||
accessed by another output command or written to a file.
|
||||
</P>
|
||||
<P>If the <I>ave</I> setting is <I>one</I>, then the values produced on timesteps
|
||||
that are multiples of <I>Nfreq</I> are independent of each other; they are
|
||||
|
|
@ -127,10 +126,10 @@ output as-is without further averaging.
|
|||
<P>If the <I>ave</I> setting is <I>running</I>, then the values produced on
|
||||
timesteps that are multiples of <I>Nfreq</I> are summed and averaged in a
|
||||
cummulative sense before being output. Each output value is thus the
|
||||
average of the value on that timestep with all preceeding values.
|
||||
This running average begins when the fix is defined; it can only be
|
||||
restarted by deleting the fix via the <A HREF = "unfix.html">unfix</A> command, or
|
||||
re-defining the fix by re-specifying it.
|
||||
average of the value produced on that timestep with all preceeding
|
||||
values. This running average begins when the fix is defined; it can
|
||||
only be restarted by deleting the fix via the <A HREF = "unfix.html">unfix</A>
|
||||
command, or re-defining the fix by re-specifying it.
|
||||
</P>
|
||||
<P>If the <I>ave</I> setting is <I>window</I>, then the values produced on
|
||||
timesteps that are multiples of <I>Nfreq</I> are summed and averaged within
|
||||
|
|
@ -176,6 +175,6 @@ ave/spatial</A>
|
|||
</P>
|
||||
<P><B>Default:</B> none
|
||||
</P>
|
||||
<P>The option defaults are style = scalar, no file output, and ave = one.
|
||||
<P>The option defaults are type = scalar, no file output, and ave = one.
|
||||
</P>
|
||||
</HTML>
|
||||
|
|
|
|||
|
|
@ -26,8 +26,6 @@ keyword = {type} or {file} or {ave} :l
|
|||
scalar = single scalar value from fix or compute
|
||||
vector = vector of values from fix or compute
|
||||
both = both a single value and vector of values from fix or compute
|
||||
{file} arg = filename
|
||||
filename = file to write results to
|
||||
{ave} args = {one} or {running} or {window M}
|
||||
one = output new average value every Nfreq steps
|
||||
running = output cummulative average of all previous Nfreq steps
|
||||
|
|
@ -90,7 +88,7 @@ timestep 200, etc.
|
|||
|
||||
:line
|
||||
|
||||
Additional optional keywords also affect the averaging.
|
||||
Additional optional keywords also affect the operation of this fix.
|
||||
|
||||
The {type} keyword chooses whether the scalar and/or vector quantities
|
||||
produced by the compute or fix are used. For a setting of {scalar} a
|
||||
|
|
@ -105,8 +103,9 @@ and/or N vector quantities are written to the file in a
|
|||
self-explanatory text format.
|
||||
|
||||
The {ave} keyword determines how the scalar and/or vector values
|
||||
produced every {Nfreq} steps are averaged with each other before they
|
||||
are accessed by another output command or written to a file.
|
||||
produced every {Nfreq} steps are averaged with values produced on
|
||||
previous steps that were multiples of {Nfreq}, before they are
|
||||
accessed by another output command or written to a file.
|
||||
|
||||
If the {ave} setting is {one}, then the values produced on timesteps
|
||||
that are multiples of {Nfreq} are independent of each other; they are
|
||||
|
|
@ -115,10 +114,10 @@ output as-is without further averaging.
|
|||
If the {ave} setting is {running}, then the values produced on
|
||||
timesteps that are multiples of {Nfreq} are summed and averaged in a
|
||||
cummulative sense before being output. Each output value is thus the
|
||||
average of the value on that timestep with all preceeding values.
|
||||
This running average begins when the fix is defined; it can only be
|
||||
restarted by deleting the fix via the "unfix"_unfix.html command, or
|
||||
re-defining the fix by re-specifying it.
|
||||
average of the value produced on that timestep with all preceeding
|
||||
values. This running average begins when the fix is defined; it can
|
||||
only be restarted by deleting the fix via the "unfix"_unfix.html
|
||||
command, or re-defining the fix by re-specifying it.
|
||||
|
||||
If the {ave} setting is {window}, then the values produced on
|
||||
timesteps that are multiples of {Nfreq} are summed and averaged within
|
||||
|
|
@ -164,4 +163,4 @@ ave/spatial"_fix_ave_spatial.html
|
|||
|
||||
[Default:] none
|
||||
|
||||
The option defaults are style = scalar, no file output, and ave = one.
|
||||
The option defaults are type = scalar, no file output, and ave = one.
|
||||
|
|
|
|||
Loading…
Reference in New Issue